The Story of Mary
by starsofimagination
Summary: Mary was about to kill Charles Augustus Magnussen, but she was interrupted. Not only were her plans ruined, but her whole life changed in that one moment. Set during His Last Vow and onwards. (Previously called In the Mind of the Assassin)
1. Chapter 1

_AN: So I might do a follow up of this, I'm not sure yet. I'm really interested in knowing what Mary was thinking and what was going through her mind during all this, so naturally, that led to this. Tah dah, enjoy!_

She had the gun pointed squarely at him. Her breath was calm and steady whereas her hostage...not so much.

"I've been waiting a long time for this," Mary said, circling the man on his knees. "Do you know how long it took me to plan this?"

"A very long time, I imagine," Charles Augustus Magnussen answered as calmly as he could. "You knew I had information on you. You had to befriend Janine and become close to her, enough so that she was your maid of honor-"

"Shut up," Mary hissed. "You're just buying yourself time. I didn't come here to chat with you."

"Then what are you going to do to me Mary?"

"I came for my files. You're going to give me everything you have on me, and then I'm going to kill you," she said softly and slowly. She looked him over. The man that no one stood up to was now at her mercy. She stopped circling him and stood in front of him.

"What will your child think of this?" Charles asked, looking up at her.

Mary pressed the gun right against his left temple. "How did you know I was pregnant?"

Charles chuckled. "I know everything, but you didn't answer my question? What will your child think of this? What will your husband think of this?"

"Do not speak to me about them. I'm doing this for them. There is nothing I wouldn't do to protect John and our child."

At that moment, Charles began to beg. "What would your husband think? Your lovely husband? Surely what would he say to you now?"

Mary shut him out. She cocked the gun and pointed it at his forehead. If he wasn't going to give her the files, she would just kill him and get them herself. She looked down at Magnussen. His mouth was still moving but no words came out. She couldn't hear him. She was too focused.

"Additionally if you're going to commit murder, you might consider changing your perfume, Lady Smallwood," came a voice from behind Mary, bringing her out of her focus.

Mary froze. She knew that voice. It couldn't be. No. This couldn't be happening now.

"Sorry, who?" Charles asked, lowering his hands and looking past Mary. "That's...not Lady Smallwood, Mr. Holmes."

She was right. It was him. Mary turned around, her gun pointed right at Sherlock. She could see the look of shock flash through his eyes in the darkened room. She suddenly felt scared. If Sherlock were here, that meant John couldn't be too far behind. John couldn't know. He must never find out about what she really was, and now, Sherlock was going to mess that all up. Damn him!

"Is John with you?" Mary asked softly.

"He's um-" Sherlock stammered.

"Is John here?" She asked again, growing impatient.

"H-He's downstairs," Sherlock answered, his eyes fixed on her.

"So, what do you do now?" Charles slowly asked. "Kill us both?"

"Mary, whatever he's got on you, let me help," Sherlock said firmly.

For a brief moment, Mary considered it, but then quickly dismissed it. Sherlock couldn't help her because then John would find out. No, she had to do this on her own. It was the only way to protect John.

"Oh Sherlock, if you take one more step I swear I will kill you," Mary threatened. She hoped that would be enough to stop him and buy herself some time.

"No, Mrs. Watson, you won't," Sherlock said, almost smugly.

Mary let out a small inaudible gasp as he began to step forward. She couldn't kill him. If she killed him and Magnussen. If she did John would be the suspect. Plus she didn't want to kill Sherlock. Sherlock was her friend. He was her husband's best friend. She already saw what his "death" did to him once. She couldn't see John go through that again. No, she had to incapacitate him. That would buy her time.

She quickly aimed and shot Sherlock on the right side of his chest. Sherlock looked down at his chest as blood started to seep through his white shirt.

"I'm sorry Sherlock, truly am," Mary said, her voice cracking every so slightly.

"Mary…" Sherlock said, his voice filled with betrayal.

Mary turned the gun away from Sherlock and back to Magnussen, her eyes still fixed on Sherlock. It was like watching him in slow motion. She watched as he fell to the ground. As soon as he was on the ground she turned and pistol whipped Magnussen hard, knocking him out cold. Grabbing her phone, she dialed 999 for an ambulance.

"You're not going to die Sherlock, not here, and not like this," She whispered more to herself. She gave him one last look and quickly left to avoid John finding her. She had much more work to do now.


	2. Chapter 2

A/N: So I decided I would continue this after all. Enjoy!

"You don't tell him," Mary told a half conscious Sherlock. She gazed down at him, feeling nothing but guilt. "You don't tell John." She moved to sit on the bed. "Sherlock," she said in a sing-song voice. "Look at me and tell me you won't tell him."

Mary watched Sherlock turn his head slightly and look at her. His eyes slowly closed and he fell back into unconsciousness. Mary sighed. It was no use of frowned and left the hospital room to join John in the hallway.

"Ready?" John asked. "What did you want to say to him anyways?"

"Oh nothing. Just sort of chastised him for getting shot," Mary teased, trying to lighten the mood before pausing. "I think he's going to be okay," she added hopefully.

"I hope so," John sighed. She could see the fear and restlessness in his eyes. "I can't wait to find the bastard who shot him. I'll kill him myself."

"I know." Mary turned away and frowned. John was going to hate her if he found out. "Let's get home. You look exhausted."

"I feel exhausted. I've been up all night with Sherlock." John took her hand and began to lead her out of the hospital. "Let's get some Thai food on the way home."

"Sounds good. I don't feel like cooking tonight." Mary smiled. She was going to at least try and enjoy what precious moments she had left with John.

XXXXX

"That was delicious," John groaned tossing away his Thai food containers into the trash bin. "That's just what I needed."

Mary laughed. "I'm glad," she responded. She kissed his cheek. "I'm going to get a shower and get ready for bed. It's been a long day. You should try and get some sleep."

"I'll be up soon," John softly said.

Mary nodded and went up to the bathroom. She must have been in the shower for at least forty-five minutes. Her mind just wouldn't stop thinking about everything that had happened. She thought about every possible outcome, everything that she could have done differently, how John would react if Sherlock told him. Not _if_, but when because she knew Sherlock would tell him. That still wasn't going to stop her from trying to bargain for his silence.

Then of course there was the baby. She placed a hand on her stomach. In a few months time she would have a baby bump. Mary sighed. Already she was screwing up the life of the child growing inside of her. She had no doubt that John would love the child and would always be there for him or her, but she didn't want her child growing up to resent her. She didn't want her child to know about her past, and if worst came to worst and she ended up in prison, she didn't want to miss out on watching her child grow up. She was stressed out, but she didn't let it show. Years of training allowed her to keep her cool under stressful times.

When she finally stepped out of the shower, she dried her hair and walked into the bedroom with nothing but a towel wrapped around her. The bedroom was dark and she could make out a figure laying in bed. It looked as though John took her advice and went to bed. She was about to pull out a pair of panties and her pajamas from a drawer when John sat up in bed.

"Come here," he said softly.

"What is it?" Mary asked curiously standing straight up with the towel still wrapped around her.

"Just come here." He patted to the spot on the bed next to him.

Mary did as he asked and sat down on the bed. Before she could say anything John turned and kissed her passionately. Mary kissed back with equal passion as John's arms snaked around her and pulled her close.

"I need you tonight," John whispered against her lips when the kiss broke.

"I'm here," Mary replied, cupping his cheek with a hand and kissing John again.

John undid the towel that was wrapped around Mary and tossed it aside. He kissed down Mary's neck slowly. She let out a soft moan and tilted her neck to give John better access. She let him lay her back on the bed and kiss down her body. He was always gentle with her, and she loved it. He began to caress and kiss her breasts before going on to worship every part of her body.

John then sat up and pulled off his own clothes before Mary brought John's lips back to her own. As she kissed him, she used her strength and rolled them over so she was now straddling him. "Let me make you feel good," she said softly as she peppered kisses down his neck. She really did want to make him feel good. After all, it was her fault he was feeling the way he was. It was her fault that his best friend nearly died.

"Please," John moaned, bringing Mary out of her thoughts. She could feel his erection against her. She shifted and kissed down his chest slowly and then back up to his lips. As she kissed him, he adjusted her hips and lined her up with his cock before slowly pushing into her. Mary moaned into John's mouth and broke the kiss to stare down into his lust filled eyes. In that moment, all worries, fears, and cares seemed to disappear. She loved him more than anything in the world and nothing else mattered.

John began to thrust into her, making her moan softly. He gripped her hips, lifting her gently as he moved. Mary leaned down and kissed and nipped at John's neck as he sped up the pace. He moaned loudly as he thrust into her, and she loved the sounds he made. It turned her on even more. Swiftly, he flipped her over so he was on top of her.

They continued to move together, their moans and whimpers filling the small bedroom. Soon John's thrusts soon became erratic as he began chanting her name. Mary's fingers dug into John's skin, gripping him tight as she reached her peak. They both called out each others' name as the climaxed together. John pulled out of her and laid down next to Mary, pulling her in his arms.

"I love you. I love you so much," John whispered, peppering her neck with kisses.

"I love you too. Always," Mary responded, her guilt now returning. She let John hold her as he fell into a peaceful sleep. "I'm sorry," she whispered. "I'm so sorry. I hope you don't completely hate me."

Soon after, Mary followed her husband into sleep.


	3. Chapter 3

"We can trust Mary."

That's what Sherlock said. Those words shocked Mary back into reality. She watched as Sherlock was lowered on to the stretcher and given oxygen. The guilt of everything weighed upon her heavily. When John looked up from Sherlock to her, she could feel nothing but a cold, icy stare. This was all her fault. If she had just been honest. If she had just gone to Sherlock to begin with this probably could have all been avoided.

"I...I need to go with him," John muttered, looking away from Mary.

"Go," she replied softly. "Go be with him."

John nodded and grabbed his coat. He gave Mary one last hard look before following the paramedics out of the flat. Mary bit her lip and wrapped her coat tightly around her. She stood there for a moment, lost in her thoughts, before leaving 221B. She took a cab back to her and John's home and locked herself inside.

She refused to cry. She couldn't do that right now. Right now she had to think clearly and plan what she was going to do next. She knew John would probably leave her. It was the sensible thing to do. John was going to read everything on the USB drive. He was going to be horrified at the things she had done. He was going to divorce her and take their child from her. The baby couldn't be raised by a monster like her.

Mary placed a hand on her stomach and blinked back tears that threatened to fall. "I'm sorry," she whispered before heading up to their...her bedroom.

She went to the closet and opened a trunk that sat inside. Inside the trunk was a false bottom that housed some of her equipment. Everything else was in a storage unit outside of the city. Mary pulled open the false bottom and pulled out several different passports all containing false identities. After she had the baby, she would have to leave. She couldn't stay here with John and the baby. She wouldn't be able to handle it.

"Well, can't go back to the states," she muttered, tossing her US passport aside. "Maybe New Zealand. Nice and far away."

She stared at the passport before sighing. Who was she kidding? She couldn't leave. She was having a baby! And she had work left to do. Magnussen wouldn't stop. He would track her down until he got what he wanted. She had to stay. Despite the current situation, John was still her husband and she needed to protect him, and Sherlock, and Molly, and all the friends she had made here.

She put the passports back in their hiding place and changed into her pajamas. She checked her phone, hoping for some sort of update only to find no new messages or calls. Sighing Mary crawled into bed and stared at the ceiling. "Fuck," she muttered, rubbing her eyes. She couldn't hold it back anymore. The tears came slowly then all at once. She sobbed into her pillow, muttering things along the line of "It's all my fault" and "John hates me."

Eventually her sobs turned to whimpers and whimpers turned to breathing. Exhaustion finally took over her and she fell into a heavy slumber

XXXXX

When Mary woke in the morning she noticed something was off. Someone had been in the house. She sat up and looked around the room. The closet door was slightly ajar. Mary furrowed her brow, slid out of bed, padded across the room, and opened the closet.

John's clothes were gone.

The next place Mary checked was the bathroom. Sure enough, all his toiletries were missing as well. She frowned and went downstairs to find a note on the refrigerator in the kitchen.

_Mary,_

_I'm moving back into 221B for the time being. I think it's best for the both of us to have some space...and I need to think everything over. I'm very very pissed off with you. You lied to me. You lied to me about everything. Even your name! That's not something I can forgive right now. I'm sorry, but I can't be with you right now._

_Please take care of yourself and our child. I would like you to send me updates from your appointments. _

_We'll talk about this later. I don't know when but we will talk about all of this._

_John _

Mary read the note over and over, crying more and more each time she read it. He was just leaving her. Just like that.

Sadness turned to fear almost immediately. She was going to go through this pregnancy alone. How was she supposed to do this by herself? She had no idea what to do. She was relying on pregnancy books and John's expertise to help her through the next nine months.

Out of anger, she crumpled the note and threw it across the room. If there was one thing she knew for sure, this was not going to be easy.


	4. Chapter 4

It had been a month since he left, but to Mary it seemed longer than that. He hadn't been at the clinic. According to Sarah he was using up his personal days. Mary wasn't surprised. Perhaps he was expecting her to quit during his time away. Well that certainly wasn't going to happen. Everything needed to appear normal. She didn't want anyone asking questions.

The house was silent only with the sound of the television in the background. There were no footsteps coming downstairs in the morning. The shower wasn't running as she went to bed at night. Breakfast wasn't being made in the morning. The routine that Mary and John had settled into was completely shattered. "Just like my marriage," Mary muttered to herself as she stared at the dirty dishes that were piling up in the sink. Usually John did them.

She stared around the living room and sighed. Everything was a mess. Take away containers littered the coffee table. Blankets and pillows covered the couch as she had taken to sleeping there inside of the bedroom, and the floor was now the home to both dirty and clean laundry. She just didn't have the energy to care or clean.

Sometimes she thought she might have been depressed. She didn't dwell on the idea, mostly because it scared her. Six years ago, before she was Mary, this wouldn't have bothered her at all. She would have been thrilled to be alone. But she wasn't that woman anymore, despite what her husband and Sherlock might think. Mary knew that she should probably go speak with someone, but she just couldn't. How does one explain her situation to someone. "I'm depressed because I'm pregnant and alone. My husband left him after he found out that I shot his best friend and was an assassin." She felt that just wouldn't go over very well.

When Mary went to sleep that night, she didn't expect to wake up to a clean house, a cup of tea, prenatal vitamins, and a note from Sherlock. She was confused and a bit shocked to be honest. After all she had shot him. She called out of him and received no answer. He hadn't been gone long because the tea was still hot. She took the vitamins and sipped her tea before reading his note.

_Mary,_

_Months ago at your wedding I made a vow to protect all three Watsons. Though you've might it slightly more difficult given your past, I plan on keeping that vow. I know John hasn't been home to help you. It's a bit idiotic to me. He's a doctor shouldn't he be concerned about your well being since you are still the mother of his child?_

_If he's not going to help, then I will. You will find that the house had been cleaned, your laundry washed, dried, sorted, and put away, your kitchen stocked, and your doctor appointments made Please note I didn't do this alone, so don't worry about my health. Wiggins helped a bit since I'm still recovering, but don't worry about that. I bear no ill feelings towards you. If I was placed in a similar situation, I think I might have done the same. After all, it was all to protect John and your child._

_Mary, you will not jeopardize the health of your child. The state you are now, however temporary, is not good for the baby. You need to go talk to someone. What's that therapist John saw? I can't care enough to remember, but go talk to her or someone? Talk to Molly or Mrs. Hudson, anyone. You can't sit here in silence waiting for John to come back. It could be some time._

_Anyways, I best be off before John notices I'm missing. I'll see you soon. I mean it Mary, take care of yourself._

_SH_

_PS: Keep Christmas open._

Mary shook her head and couldn't help but smile. Sherlock was everything she always thought he was. She was grateful that someone still cared, even if he would deny that he did care.

"What does he want with Christmas though?" She asked herself. She shrugged and pushed the thought away before going to take a shower. After getting dressed and ready for the day, she grabbed her phone, scrolled through her contacts, and pressed the call button for the one she had been looking for.

"Molly? It's Mary. Are you free for lunch today?"


End file.
